First let me say, I found your post because I have the same kind of problem and was looking for an answer. After changing CO2 canisters, my regulator became difficult to set just right. I wound up flooding my nano w/CO2. As the drop checker turned yellower, the Ammonia Alert tag I have in the tank went from showing 0 NH3 to 0.2 ppm. There are no fish in the tank.
Having found no answer to the issue, I googled CO2 and NH3. After reading several journal papers on industrial CO2 emissions and NH3 which are way over my head, I have seen that there is a definite correlative relationship between NH3 and CO2, the more CO2 you have, the more NH3 can be produced. Also, I found this handy-dandy equation which I'm sure would explain it if it weren't 3AM and I was coherent enough to rearrange the factors to show what occurs in the aquarium:
2NH3 + CO2 --> (NH2)2CO + H2O
My understanding is that the equation would show (if you reverse it) that when you put CO with H2O and some source of N, you will get NH3 as a byproduct. I guess it's just not a relevant amount in the aquarium unless you overdo it on the CO2.
If you don't have a drop checker or other CO2 test, get one. There's no need to waste CO2 if you're dosing too much like I accidentally did. If you're not overdosing CO2, maybe you have too much N from ferts?
Hope this helps. If someone else has a better explanation of the CO2-NH3 relationship, please chime in!